OBO-Edit: Code Overhaul

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Important changes in the OBO-Edit 1.2 Codebase

Now that OBO-Edit is being developed on Eclipse, we have taken advantage of Eclipse's code-refactoring capabilities to implement some long-overdue cleanups in OBO-Edit's code. These changes are going into the repository immediately, but they will become part of an official release as of OBO-Edit 1.2.

1) Many methods and classes renamed - OBO-Edit contained a number of methods and classes that were ported from DAG-Edit, and retained DAG-Edit-centric class and method names. Many of these objects have been renamed using the Eclipse-refactor capability. The changes include:

  • org.geneontology.oboedit.gui
    • DEPlugin becomes ComponentPlugin
    • DEEditorFrame becomes MainFrame
    • DESplashScreen becomes SplashScreen
  • org.geneontology.oboedit.dataadapter
    • GOBOParseEngine becomes OBOParseEngine
    • GOBOParseException becomes OBOParseException
    • GOBOParser becomes OBOParser
    • GOBOSimpleParser becomes OBOSimpleParser
    • GOBOVersionSpec becomes OBOVersionSpec
  • org.geneontology.oboedit.event
    • DEHistoryAppliedEvent becomes HistoryAppliedEvent
    • DEHistoryListener becomes HistoryListener
    • DEPluginEvent becomes PluginEvent
    • DEPluginListener becomes PluginListener
    • DESubSelectEvent becomes SubSelectEvent
    • DESubSelectEvent.getTerm() becomes SubSelectEvent.getSelectedObject()
    • DESubSelectListener becomes SubSelectListener
    • DETermReloadEvent becomes RefreshEvent
    • DETermReloadListener becomes RefreshListener
    • DETermSelectEvent becomes SelectionEvent
    • DETermSelectListener becomes SelectionListener

2) Deadwood classes & methods deleted - OBO-Edit's architecture has evolved over time, and some vestigial classes and methods remain from earlier versions. All unused classes were entirely removed (ie the defunct org.geneontology.oboedit.filters package), but some other unused (but still compiling) classes and methods have also been removed:

  • org.geneontology.oboedit.gui.event
    • DisableGUIEvent, DisableGUIListener, Controller.fireDisableGUIEvent() and referencing code has been removed
  • org.geneontology.oboedit.dataadapter
    • DEDataAdapterI
    • DefaultIDAdapter
    • GOSerialAdapter - use SerialAdapter instead
    • GOSerialGUI
    • OWLAdapter - this is an old, non-functioning piece of experimental code
    • SingleFileAdapter
    • SingleFileAdapterI
    • SingleFileGUI
    • SingleTermSerializerI

3) New Build System - OBO-Edit now builds using Ant. The old makefile-based system is no longer supported.